[R-sig-Debian] updating r-cran- packages on a new Ubuntu lucid system

Michael Friendly friendly at yorku.ca
Tue Feb 1 16:56:05 CET 2011

On 1/31/2011 12:14 PM, Dirk Eddelbuettel wrote:
> On 31 January 2011 at 09:04, Michael Friendly wrote:
> | I'm not any further ahead in trying to update vcd from 1.2-7 to 1.2-9.
> | How can I resolve this?
> If what you're doing doesn't work, do something else.   The .deb package are
> convenient.  They can't all be recent because, well, a distro has release
> schedules.
OK:   I used (as sudo)
and it seemed to work;  however old.packages() still reports vcd at 
1.2-7.  Why is that?

 > library(vcd)
Loading required package: MASS
Loading required package: grid
Loading required package: colorspace
 > sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-pc-linux-gnu (64-bit)

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] vcd_1.2-9        colorspace_1.0-1 MASS_7.3-9

loaded via a namespace (and not attached):
[1] tools_2.12.1
 > old.packages()
     Package LibPath                   Installed Built    ReposVer
rgl "rgl"   "/usr/lib/R/site-library" "0.89"    "2.10.1" "0.92.798"
vcd "vcd"   "/usr/lib/R/site-library" "1.2-7"   "2.9.2"  "1.2-9"
rgl "http://probability.ca/cran/src/contrib"
vcd "http://probability.ca/cran/src/contrib"

In addition, some follow up questions, unanswered by reading 
/bin/linux/ubuntu/README.  I'm persisting
in this because I'm setting up a new system, and want to insure that I 
don't create maintenance problems
down the road.

(a) At present, I have access to this machine only via a remote terminal 
window; no X11.  Is there any way
to install a package like r-cran-rgl that seems to require X11?

(b) It seems to be recommended to maintain the distinction between 
r-cran-* packages, which I should install
  as root via apt-get and non-r-cran packages, which I should install in 
R_LIBS_USER = "~/lib/R/library" as my normal user.
  Is this correct?
  I'm the only R user on this machine, so it seems simpler to install 
*all* packages as root and let them go into

     Q: will this cause any problems with apt-get upgrade finding 
non-cran-r packages there?

Alternatively, if I try to install non-cran packages via 
install.packages() as my normal user,

     Q: How to distinguish, in R, r-cran from non-r-cran packages?
     Q: How to handle dependencies, where a non-cran package requires an 
r-cran one?

e.g., in Windows, I would just run the following to install a bunch of 
(non-cran) packages, and be done with it.

mypkgs <- c("vcdExtra", "HistData", "candisc", "tableplot", "Guerry", 

otherpkgs <-c("ca", "catspec", "coin", "corrgram", "gmodels", "gnm", 
"ggplot2", "plyr", "sem")

allpkgs <- union(mypkgs, otherpkgs)

# install the above, along with any dependencies
install.packages(allpkgs, dependencies=TRUE)
# update any recently modified packages

Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

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